BACKGROUND: The contribution of gut microbiota to human high-altitude adaptation remains inadequately understood.
METHODS: Here a comparative analysis of gut microbiota was conducted between healthy individuals living at sea level and high altitude using deep whole-metagenome shotgun sequencing, to investigate the adaptive mechanisms of gut microbiota in plateau inhabitants.
RESULTS: The results showed the gut bacteriomes in high-altitude individuals exhibited greater within-sample diversity and significant alterations in both bacterial compositional and functional profiles when compared to those of sea-level individuals, indicating the potential selection of unique bacteria associated with high-altitude environments. The strain-level investigation revealed enrichment of Collinsella aerofaciens and Akkermansia muciniphila in high-altitude populations. The characteristics of gut virome and gut mycobiome were also investigated. Compared to sea-level subjects, high-altitude subjects exhibited a greater diversity in their gut virome, with an increased number of viral operational taxonomic units (vOTUs) and unique annotated genes. Finally, correlation analyses revealed 819 significant correlations between 42 bacterial species and 375 vOTUs, while no significant correlations were observed between bacteria and fungi or between fungi and viruses.
CONCLUSIONS: The findings have significantly contributed to an enhanced comprehension of the mechanisms underlying the high-altitude geographic adaptation of the human gut microbiota.

Biotransformation is a major dissipation process of tetrabromobisphenol A and its derivatives (TBBPAs) in soil. The biotransformation and ultimate environmental fate of TBBPAs have been widely studied, yet the effect of root exudates (especially low-molecular weight organic acids (LMWOAs)) on the fate of TBBPAs is poorly documented. Herein, the biotransformation behavior and mechanism of TBBPAs in bacteriome driven by LMWOAs were comprehensively investigated. Tartaric acid (TTA) was found to be the main component of LMWOAs in root exudates of Helianthus annus in the presence of TBBPAs, and was identified to play a key role in driving shaping bacteriome. TTA promoted shift of the dominant genus in soil bacteriome from Saccharibacteria_genera_incertae_sedis to Gemmatimonas, with a noteworthy increase of 24.90-34.65% in relative abundance of Gemmatimonas. A total of 28 conversion products were successfully identified, and β-scission was the principal biotransformation pathway for TBBPAs. TTA facilitated the emergence of novel conversion products, including 2,4-dibromophenol, 3,5-dibromo-4-hydroxyacetophenone, para-hydroxyacetophenone, and tribromobisphenol A. These products were formed via oxidative skeletal cleavage and debromination pathways. Additionally, bisphenol A was observed during the conversion of derivatives. This study provides a comprehensive understanding about biotransformation of TBBPAs driven by TTA in soil bacteriome, offering new insights into LMWOAs-driven biotransformation mechanisms.

The vaginal microbiota plays an important role in the health of the female reproductive tract and is closely associated with various pregnancy outcomes and sexually transmitted diseases. Plenty of internal and external factors have strong influence on the changes in a woman\'s vaginal microbiome. However, the effect of a high-altitude on female vaginal microbiota has not been described. In this study, we characterized the vaginal bacteriome and virome of 13 and 34 healthy women living in high-altitude and sea-level areas, using whole-metagenome shotgun sequencing of their vaginal mucus samples. The results revealed that the vaginal bacteriomes of high-altitude individuals are featured by a significant increase of species diversity, depletion of Lactobacillus crispatus, and more abundant of some anaerobic bacteria, such as Chlamydia trachomatis, Mageeibacillus indolicus, Dialister micraerophilus, and Sneathia amnii). In addition, the vagina samples of sea-level subjects harbor more Lactobacillus strains, whereas the anaerobic bacteroidetes strains mostly appeared in high-altitude subjects. Identified and assembled 191 virus operational taxonomic units (vOTUs), there were significant differences in the abundance of 107 vOTUs between the two groups. Together, the results of this study raised the understanding of bacteriome and virome in the vagina of women at different elevations, and demonstrated that the vaginal microbiome is related to the high-altitude geographic adaptation.

Emerging evidence suggests autism spectrum disorder (ASD) is associated with altered gut bacteria. However, less is known about the gut viral community and its role in shaping microbiota in neurodevelopmental disorders. Herein, we perform a metagenomic analysis of gut-DNA viruses in 60 children with ASD and 64 age- and gender-matched typically developing children to investigate the effect of the gut virome on host bacteria in children with ASD. ASD is associated with altered gut virome composition accompanied by the enrichment of Clostridium phage, Bacillus phage, and Enterobacteria phage. These ASD-enriched phages are largely associated with disrupted viral ecology in ASD. Importantly, changes in the interplay between the gut bacteriome and virome seen in ASD may influence the encoding capacity of microbial pathways for neuroactive metabolite biosynthesis. These findings suggest an impaired bacteriome-virome ecology in ASD, which sheds light on the importance of bacteriophages in pathogenesis and the development of microbial therapeutics in ASD.

The successful large-scale cultivation of morel mushrooms (Morchella sextelata) requires a comprehensive understanding of the soil bacterial communities associated with morel-farming beds, as the interactions between fungi and bacteria play a crucial role in shaping the soil microbiome. In this study, we investigated the temporal distribution and ecological characteristics of soil bacteria associated with morel fruiting bodies at different stages, specifically the conidial and primordial stages, under two cropping regimes, non-continuous cropping (NCC) and continuous cropping (CC). Our findings revealed a significant reduction in the yield of morel primordia during the third year following 2 years of CC (0.29 ± 0.25 primordia/grid), in comparison to the NCC regime (12.39 ± 6.09 primordia/grid). Furthermore, inoculation with morel mycelia had a notable impact on soil bacterial diversity, decreasing it in the NCC regime and increasing the number of generalist bacterial members in the CC regime. The latter regime also led to the accumulation of nutrients in the soil beds, resulting in a shift from a stochastic to a deterministic process in the composition of the bacterial community, which differed from the NCC regime. Additionally, mycelial inoculation had a positive effect on the abundance of potential copiotrophic/denitrifying and N-fixing bacteria while decreasing the abundance of oligotrophic/nitrifying bacteria. Interestingly, this effect was more pronounced in the NCC regime than in the CC regime. These results suggest that the increase in potential copiotrophic/denitrifying and N-fixing bacteria facilitated the decomposition of nutrients in exogenous nutrient bags by morel mushrooms, thereby maintaining nitrogen balance in the soil. Overall, our study provides valuable insights into the interactions between morel mycelia and the associated soil bacteriome as well as the influence of different cultivation regimes on these interactions. These findings contribute to our understanding of the complex dynamics of the soil microbiome and can inform strategies for optimizing morel mushroom cultivation.

Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT.
We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network.
Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract.

Rapid aerobic decomposition and a high cost/benefit ratio restrain the transformation of Chinese cabbage waste into livestock feed. Herein, anaerobically co-fermenting Chinese cabbage waste with wheat bran and rice bran at different dry matter levels (250, 300, 350 g/kg fresh weight) was employed to achieve the effective and feasible clean transformation of Chinese cabbage waste, and the related microbiological mechanisms were revealed by high-throughput sequencing technology. The bran treatments caused an increase in pH value (4.75-77.25%) and free amino acid content (12.09-152.66%), but a reduction in lactic acid concentration (54.58-77.25%) and coliform bacteria counts (15.91-20.27%). In addition, the wheat bran treatment improved the levels of short-chain fatty acids, nonprotein nitrogen, water-soluble carbohydrates and antioxidant activity and reduced the ammonia nitrogen contents. In contrast, the rice bran treatment decreased the levels of acetic acid, water-soluble carbohydrates, nonprotein nitrogen, ammonia nitrogen, and antioxidant activities. Microbiologically, the bran treatments stimulated Pediococcus, Lactobacillus, Enterobacter, and Weissella but inhibited Lactococcus and Leuconostoc, which were the primary organic acid producers reflected by the redundancy analysis. In addition, Chinese cabbage waste fermented with wheat bran at 350 g/kg fresh weight or with rice bran at 300 g/kg fresh weight increased the scale and complexity of bacteriome, promoted commensalism or mutualism and upregulated the global metabolism pathways, including carbohydrate and amino acid metabolisms. Furthermore, the bran treatments resulted in an increase in bacterial communities that were facultatively anaerobic, biofilm-formed, Gram-negative, potentially pathogenic and stress-tolerant. Collectively, the bran treatments inhibited effluent formation and protein degradation and improved nutrient preservation but reduced organic acid production during the anaerobic fermentation, which is linked to the variations in the bacteriome, indicating that the constructed fermentation system should be further optimized.

The effects of glucose, fructose, sucrose and molasses on organic acid levels, protein degradation, nutrient preservation and bacteriome were studied during the anaerobic fermentation of Chinese cabbage waste. The results showed that fructose and molasses additions caused a significant (p < 0.05) increase in lactic acid production (82.16-89.79 %), acetic acid production (175.41-196.93 %), ammonia nitrogen formation (15.93-37.43 %) and reduction of neutral detergent fiber level (8.17-15.87 %). However, few positive effects of glucose and sucrose additions were found on organic acid production. Furthermore, carbon source additions enriched (p < 0.05) the acid-producing bacteria, such as Lactobacillus paralimentarius and Lactobacillus heilongjiangensis, upregulated (p < 0.05) the pathways of carbohydrate and lipid metabolisms and reduced (p < 0.05) the abundances of Lactobacillus buchneri and Escherichia coli and bacteria that were mobile elements-contained and stress-tolerant. Collectively, fructose and molasses additions enhanced the recycling of Chinese cabbage waste by anaerobic fermentation, in which the desired products are organic acids.

Oral microbial dysbiosis contributes to the development of oral squamous cell carcinoma (OSCC). Numerous studies have focused on variations in the oral bacterial microbiota of patients with OSCC. However, similar studies on fungal microbiota, another integral component of the oral microbiota, are scarce. Moreover, there is an evidence gap regarding the role that microecosystems play in different niches of the oral cavity at different stages of oral carcinogenesis. Here, we catalogued the microbial communities in the human oral cavity by profiling saliva, gingival plaque, and mucosal samples at different stages of oral carcinogenesis. We analyzed the oral bacteriome and mycobiome along the health-premalignancy-carcinoma sequence. Some species, including Prevotella intermedia, Porphyromonas endodontalis, Acremonium exuviarum, and Aspergillus fumigatus, were enriched, whereas others, such as Streptococcus salivarius subsp. salivarius, Scapharca broughtonii, Mortierella echinula, and Morchella septimelata, were depleted in OSCC. These findings suggest that an array of signature species, including bacteria and fungi, are closely associated with oral carcinogenesis. OSCC-associated diversity differences, species distinction, and functional alterations were most remarkable in mucosal samples, not in gingival plaque or saliva samples, suggesting an urgent need to define oral carcinogenesis-associated microbial dysbiosis based on the spatial microbiome. IMPORTANCE Abundant oral microorganisms constitute a complex microecosystem within the oral environment of the host, which plays a critical role in the adjustment of various physiological and pathological states of the oral cavity. In this study, we demonstrated that variations in the \"core microbiome\" may be used to predict carcinogenesis. In addition, sample data collected from multiple oral sites along the health-premalignancy-carcinoma sequence increase our understanding of the microecosystems of different oral niches and their specific changes during oral carcinogenesis. This work provides insight into the roles of bacteria and fungi in OSCC and may contribute to the development of early diagnostic assays and novel treatments.

Understanding the role of fecal microbiota transplantation (FMT) in the decolonization of multidrug-resistant organisms (MDRO) is critical. Specifically, little is known about virome changes in MDRO-infected subjects treated with FMT. Using shotgun metagenomic sequencing, we characterized longitudinal dynamics of the gut virome and bacteriome in three recipients who successfully decolonized carbapenem-resistant Enterobacteriaceae (CRE), including Klebsiella spp. and Escherichia coli, after FMT. We observed large shifts of the fecal bacterial microbiota resembling a donor-like community after transfer of a fecal microbiota dominated by the genus Ruminococcus. We found a substantial expansion of Klebsiella phages after FMT with a concordant decrease of Klebsiella spp. and striking increase of Escherichia phages in CRE E. coli carriers after FMT. We also observed the CRE elimination and similar evolution of Klebsiella phage in mice, which may play a role in the collapse of the Klebsiella population after FMT. In summary, our pilot study documented bacteriome and virome alterations after FMT which mediate many of the effects of FMT on the gut microbiome community. IMPORTANCE Fecal microbiota transplantation (FMT) is an effective treatment for multidrug-resistant organisms; however, introducing a complex mixture of microbes also has unknown consequences for landscape features of gut microbiome. We sought to understand bacteriome and virome alterations in patients undergoing FMT to treat infection with carbapenem-resistant Enterobacteriaceae. This finding indicates that transkingdom interactions between the virome and bacteriome communities may have evolved in part to support efficient FMT for treating CRE.